Tree Genetics & Genomes

, Volume 9, Issue 5, pp 1143–1150 | Cite as

Development of male-specific SCAR marker in date palm (Phoenix dactylifera L.)

Original Paper

Abstract

Genetics of control mechanisms that underlies sex differentiation in date palm is not known. Sex of the plants becomes known only at the time of first flowering, which takes around 5 years. In comparison, molecular diagnosis (if available/feasible) promises quick and reliable identification of sex types very early when plantlets are growing in seedbeds. To develop such an assay, genomic DNA from 45 individual plants (25 female and 20 male) belonging to different varieties of date palm was subjected to PCR amplification using 100 random amplified polymorphic DNA (RAPD) and 104 intersimple sequence repeat (ISSR) primers. Initially, two bulk genomic DNA samples (each made by pooling DNA from ten male and female plants, separately) were used. A primer showing sex-specific band in bulked samples was further used for amplification of the genomic DNA of the individual samples of that bulk. Only one RAPD primer, OPA-02, amplified a fragment of ~1.0 kb in all the individual samples of male genotypes, whereas this fragment was absent in all the female genotypes. This male-specific fragment was cloned and sequenced (GenBank accession no. JN123357), and a sequence-characterized amplified region (SCAR) primer pair was designed that amplified a 406-bp fragment in both female and male genotypes and a unique fragment of 354 bp in only male genotypes. The SCAR marker was further validated using 25 female and ten male date palm plants belonging to different varieties collected from different locations.

Keywords

Date palm Sex-specific marker RAPD ISSR SCAR Sex diagnosis 

Supplementary material

11295_2013_617_MOESM1_ESM.doc (242 kb)
ESM 1(DOCX 242 docx)

References

  1. Agarwal M, Shrivastava N, Padh H (2011) Development of sex linked AFLP markers in Simmondsia chinensis. Plant Breeding 130(1):114–116CrossRefGoogle Scholar
  2. Agrawal V, Sharma K, Gupta S, Kumar R, Prasad M (2007) Identification of sex in Simmondsia chinensis (jojoba) using RAPD markers. Plant Biotech Rep 1(4):207–210CrossRefGoogle Scholar
  3. Banerjee NS, Manoj P, Das MR (1999) Male-sex-associated RAPD markers in Piper longum L. Curr Sci 77(5):693–695Google Scholar
  4. Bedoya GC, Nunez V (2007) A SCAR marker for the sex types determination in Colombian genotypes of Carica papaya. Euphytica 153:215–220CrossRefGoogle Scholar
  5. Deputy JC, Ming R, Ma H, Liu Z, Fitch MM, Wang M, Manshardt R, Stiles JI (2002) Molecular markers for sex determination in papaya (Carica papaya L.). Theor Appl Genet 106:107–111PubMedGoogle Scholar
  6. Gangopadhyay G, Roy SK, Kaushik G, Poddar R, Bandyopadhyay T, Basu D, Mukherjee KK (2007) Sex detection of Carica papaya and Cycus circinalis in pre-flowering stage by ISSR and RAPD. Curr Sci 92:524–526Google Scholar
  7. Gill GP, Harvey CF, Gardner RC, Fraser LG (1998) Development of sex-linked PCR markers for gender identification in Actinidia. Theor Appl Genet 97:439–445CrossRefGoogle Scholar
  8. Gunter LE, Roberts GT, Lee K, Larimer FW, Tuskan GA (1998) RAPD and SCAR markers linked to femaleness in Salix viminalis L. Plant and Animal Genome VI Conference P362Google Scholar
  9. Hormaza JI, Dollo L, Polito VS (1994) Identification of a RAPD marker linked to sex determination in Pistacio vera using bulked segregant analysis. Theor Appl Genet 89:9–13CrossRefGoogle Scholar
  10. Ince AG, Karaca M, Onus AN (2010) A reliable gender diagnostic PCR assay for jojoba (Simmondsia chinensis (Link) Schneider). Genet Resour Crop Evol 57(5):773–779CrossRefGoogle Scholar
  11. Khadka DK, Nejidat A, Tal M, Goldhirsh GA (2002) DNA markers for sex: molecular evidence for gender dimorphism in dioecious Mercurialis annua. Mol Breed 9:251–257CrossRefGoogle Scholar
  12. Li M, Yang H, Li F, Yang F, Yin G, Gan S (2010) A male-specific SCAR marker in Calamus simplicifolius, a dioecious rattan species endemic to China. Mol Breed 25:549–551CrossRefGoogle Scholar
  13. Liao L, Liu J, Dai Y, Li Q, Xie M, Chen Q, Yin H, Qiu G, Liu X (2009) Development and application of SCAR markers for sex identification in the dioecious species Ginkgo biloba L. Euphytica 169:49–55CrossRefGoogle Scholar
  14. Maki M (2009) Development of SCAR markers for sex determination in the dioecious shrub Aucuba japonica (Cornaceae). Genome 52:231–237PubMedCrossRefGoogle Scholar
  15. Mandolino G, Carboni A, Forapani S, Faeti V, Ranalli P (1998) Identification of DNA markers linked to the male sex in dioecious hemp (Cannabis sativa L.). Theor Appl Genet 98:86–92. doi:10.1007/s001220051043 CrossRefGoogle Scholar
  16. Mitra C, Kharb P, Uppal S, Jain S (2011) Genetic diversity analysis in date palm (Phoenix dactylifera L.): a comparative assessment of ISSR and RAPD marker assays. J Hort Sci & Biotech 86(4):398–402Google Scholar
  17. Mohsenzadeh H, Pasalari H (2010) Identification of a male-specific RAPD marker in Phoenix dactylifera. J Hort Sci & Biotech 85(2):144–146Google Scholar
  18. Mulcahy DL, Weeden NF, Kesseli R, Carroll SB (1992) DNA probes for the Y chromosome of Silene latifolia, a dioecious angiosperm. Sex Plant Reprod 5:86–88CrossRefGoogle Scholar
  19. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acid Res 8:4321–4326PubMedCrossRefGoogle Scholar
  20. Paran I, Michelmore RW (1993) Development of reliable PCR based markers linked to downy mildew resistance genes in lettuce. Theor Appl Genet 85(8):985–993CrossRefGoogle Scholar
  21. Parasnis AS, Gupta VS, Tamhankar SA, Ranjekar PK (2000) A highly reliable sex diagnostic PCR assay for mass screening of papaya seedlings. Mol Breed 6:337–344CrossRefGoogle Scholar
  22. Qacif N, Baaziz M, Bendiab K (2007) Biochemical investigations on peroxidase contents of male and female inflorescences of date palm (Phoenix dactylifera L.). Sci Hortic (Amsterdam) 114:298–301CrossRefGoogle Scholar
  23. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allerd RW (1984) Ribosomal spacer length polymorphism in barley: Mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA 81:8014–8018PubMedCrossRefGoogle Scholar
  24. Shibu MP, Ravishankar KV, Anand L, Ganeshaiah KN, Shaanker U (2001) Identification of sex-specific DNA markers in the dioecious tree, nutmeg (Myristica fragrans Houtt.). PGR Newsl 121:59–61Google Scholar
  25. Shirkot P, Sharma DR, Mohapatra T (2002) Molecular identification of sex in Actinidia deliciosa var. deliciosa by RAPD markers. Sci Hortic 94:33–39CrossRefGoogle Scholar
  26. Siljak-Yakovlev S, Cerbah M, Sarr A, Benmalek S, Bounaga N, Coba de la Pena T, Brown SC (1996) Chromosomal sex determination and heterochromatin structure in date palm. Sex Plant Reprod 9(3):127–132CrossRefGoogle Scholar
  27. Singh P, Kharb P, Pandey N, Batra P, Khatak S, Dhillon S, Uppal S, Chowdhury VK (2006) RAPD analysis for genetic diversity and identification of sex-specific marker in date palm (Phoenix dactylifera L.). Haryana J of Hort Sci 35:232–234Google Scholar
  28. Torjek O, Bucherna N, Kiss E, Homoki H, Finta-Korpelova Z, Bócsa I, Heszky LE (2002) Novel male-specific molecular markers (MADC5, MADC6) in hemp. Euphytica 127:209–218CrossRefGoogle Scholar
  29. Xu Y, Shimoro X, Hofstra H (1994) Plant DNA isolation protocol. Nucleic Acids Res 22:2399–2403PubMedCrossRefGoogle Scholar
  30. Yakubou B, Barazani O, Golan-Goldhirsh A (2005) Combination of SCAR primers and touchdown-PCR for sex identification in Pistacia vera L. Sci Hort 103:473–478CrossRefGoogle Scholar
  31. Yang H, Si-Ming G, Huang-Tian Y, Huang-Can X (2005) Identification of random amplified polymorphic DNA markers linked to sex determination in Calamus simplicifolius. J Integr Plant Biol 47:1249–1253CrossRefGoogle Scholar
  32. Younis RAA, Ismail OM, Soliman SS (2008) Identification of sex-specific DNA markers for date palm (Phoenix dactylifera L.). Res J Agric Biol Sci 4(4):278–284Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Department of Molecular Biology & BiotechnologyCCS Haryana Agricultural UniversityHisarIndia
  2. 2.Centre for Plant BiotechnologyCCS Haryana Agricultural UniversityHisarIndia
  3. 3.Molecular Marker LaboratoryCentre for Cellular and Molecular Biology (CSIR-CCMB)TarnakaIndia
  4. 4.Department of GeneticsCCS Haryana Agricultural UniversityHisarIndia
  5. 5.Molecular Genetics LaboratoryCentre for Cellular and Molecular Biology (CSIR-CCMB)TarnakaIndia

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